Hi Chris,
Not sure if this is any help to you or not…
I machine many circuit boards and often use different CAD/CAM software to create the layouts. As the problem of scale is always a possibility I now include in the layout an outside border, of known dimension, around the pcb (or two outside markers of known distance).
Once the GCode has been loaded into Mach3 the Toolpath tab shows the Program Limits (size of my border or distance between markers) I then, if necessary, adjust the X and Y Scale DRO’s (main screen) to get the size correct (just a simple calculation required here).
Tweakie.